Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A5 F28 I2 R1
|
721 |
0.0 |
1472758 |
54.8% |
807071 |
56.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,273,453 |
(A)5→6 |
coding (448/714 nt) |
aphA → |
acid phosphatase/phosphotransferase, class B, non‑specific |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,273,448 | 1 | . | A | 76.9%
| 49.5
/ 17.0
| 26 | coding (443/714 nt) | aphA | acid phosphatase/phosphotransferase, class B, non‑specific |
| Reads supporting (aligned to +/- strand): ref base . (6/0); new base A (0/20); total (6/20) |
| Fisher's exact test for biased strand distribution p-value = 4.34e-06 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.77e-01 |
TCTTCTTTGTGACTGGTCGTAGCCCGACGAAAACAGAAACGGTTTC‑AAAAACGCTGGCGGATAATTTTCATA > W3110S.gb/4273403‑4273474
|
tcttctTTGTGACTGGTCGTAGCCCGACGAAAACAGAAACGGTTTC‑AAAAACGCTGGCGGAt > 1:1168479/1‑62 (MQ=255)
tcttctTTGTGACTGGTCGTAGCCCGACGAAAACAGAAACGGTTTC‑AAAAACGCTGGCGGAt > 1:769319/1‑62 (MQ=255)
tcttctTTGTGACTGGTCGTAGCCCGACGAAAACAGAAACGGTTTC‑AAAAACGCTGGCGGAt > 1:548017/1‑62 (MQ=255)
tcttctTTGTGACTGGTCGTAGCCCGACGAAAACAGAAACGGTTTC‑AAAAACGCTGGCGGAt > 1:526254/1‑62 (MQ=255)
tcttctTTGTGACTGGTCGTAGCCCGACGAAAACAGAAACGGTTTC‑AAAAACGCTGGCGGAt > 1:469039/1‑62 (MQ=255)
tcttatTTGTGACTGGTCGTAGCCCGACGAAAACAGAAACGGTTTC‑AAAAACGCTGGCGGAt > 1:702172/1‑62 (MQ=255)
ggTCGTAGCCCGACGAAGACAGAAACGGTTTCAAAAAACGCTGGCGGATAATTTTCata < 1:845461/59‑1 (MQ=255)
ggTCGTAGCCCGACGAAAACAGAAACGGTTTCAAAAAACGCTGGCGGATAATTTTCata < 1:578755/59‑1 (MQ=255)
ggTCGTAGCCCGACGAAAACAGAAACGGTTTCAAAAAACGCTGGCGGATAATTTTCata < 1:94525/59‑1 (MQ=255)
ggTCGTAGCCCGACGAAAACAGAAACGGTTTCAAAAAACGCTGGCGGATAATTTTCata < 1:915274/59‑1 (MQ=255)
ggTCGTAGCCCGACGAAAACAGAAACGGTTTCAAAAAACGCTGGCGGATAATTTTCata < 1:1088097/59‑1 (MQ=255)
ggTCGTAGCCCGACGAAAACAGAAACGGTTTCAAAAAACGCTGGCGGATAATTTTCata < 1:730939/59‑1 (MQ=255)
ggTCGTAGCCCGACGAAAACAGAAACGGTTTCAAAAAACGCTGGCGGATAATTTTCata < 1:705859/59‑1 (MQ=255)
ggTCGTAGCCCGACGAAAACAGAAACGGTTTCAAAAAACGCTGGCGGATAATTTTCata < 1:674534/59‑1 (MQ=255)
ggTCGTAGCCCGACGAAAACAGAAACGGTTTCAAAAAACGCTGGCGGATAATTTTCata < 1:599372/59‑1 (MQ=255)
ggTCGTAGCCCGACGAAAACAGAAACGGTTTCAAAAAACGCTGGCGGATAATTTTCata < 1:1313022/59‑1 (MQ=255)
ggTCGTAGCCCGACGAAAACAGAAACGGTTTCAAAAAACGCTGGCGGATAATTTTCata < 1:5740/59‑1 (MQ=255)
ggTCGTAGCCCGACGAAAACAGAAACGGTTTCAAAAAACGCTGGCGGATAATTTTCata < 1:1199761/59‑1 (MQ=255)
ggTCGTAGCCCGACGAAAACAGAAACGGTTTCAAAAAACGCTGGCGGATAATTTTCata < 1:497154/59‑1 (MQ=255)
ggTCGTAGCCCGACGAAAACAGAAACGGTTTCAAAAAACGCTGGCGGATAATTTTCata < 1:1265789/59‑1 (MQ=255)
ggTCGTAGCCCGACGAAAACAGAAACGGTTTCAAAAAACGCTGGCGGATAATTTTCata < 1:268896/59‑1 (MQ=255)
ggTCGTAGCCCGACGAAAACAGAAACGGTTTCAAAAAACGCTGGCGGATAATTTTCata < 1:249744/59‑1 (MQ=255)
ggTCGTAGCCCGACGAAAACAGAAACGGTTTCAAAAAACGCTGGCGGATAATTTTCata < 1:15948/59‑1 (MQ=255)
ggTCGTAGCCCGACGAAAACAGAAACGGTTTCAAAAAACGCTGGCGGATAATTTTCata < 1:142915/59‑1 (MQ=255)
gTCGTAGCCCGACGAAAACAGAAACGGTTTCAAAAAACGCTGGCGGATAATTTTCata < 1:1208843/58‑1 (MQ=255)
cccGACGAAAACAGAAACGGTTTCAAAAAACGCTGGCGGATAATTTTCata < 1:713119/51‑1 (MQ=255)
|
TCTTCTTTGTGACTGGTCGTAGCCCGACGAAAACAGAAACGGTTTC‑AAAAACGCTGGCGGATAATTTTCATA > W3110S.gb/4273403‑4273474
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
